ABSTRACT
Codon usage in 87 602 genes has been calculated using the nucleotide sequence
data obtained from the GenBank Genetic Sequence Data Bank (Release 90.0;
September 1995). The database is called the CUTG Database; the complete form of
the database can be obtained by anonymous ftp from DDBJ and a part of the
database, which lists the frequency of codon use in each organism, is made
searchable through our World Wide Web server.
Codon usage in individual genes has been calculated using the nucleotide
sequence data obtained from the GenBank Genetic Sequence Data Bank (Release
90.0; September 1995). The compilation of codon usage is synchronized with each
major release of GenBank. The resulting database is called the CUTG database (
1
-
5
).
In selecting protein coding sequences we relied on the FEATURES tables of
GenBank, and only complete genes without unambiguous bases were used in the
analysis. In GenBank, a group of consecutive genes whose entire region had been
sequenced were registered under one LOCUS name. To distinguish the different
genes belonging to a single LOCUS, the symbol # followed by a number is added
after the LOCUS name; the numbers represent the order of the CDS registered in
the FEATURES table of GenBank. When introns of a gene have not been completely
sequenced, some of its exons are registered in separate entries (LOCUS) in
GenBank. These exons, belonging to the same gene but having different LOCUS
names, were combined into one entry and the first LOCUS name is added.
For the biological significance of codon usage, see Ikemura (
6
) and Aota and Ikemura (
7
,
8
).
Files of the present database, containing codon usage of 87 602 CDSs of 4805
species, are available by anonymous ftp from DDBJ. Files named as gb***.codon
list the codon use in each gene registered in the GenBank Sequence files
(gb***.seq). The LOCUS names given in GenBank were used to designate individual
genes. Each LOCUS name is followed by fields of information extracted from the
FEATURES of each CDS for defining each open reading frame analyzed here. The
order of the codons in the table is the same as the previous compilation (see
the CODON_LABEL file or REFERENCES).
To reveal the characteristics of codon use of a wide range of organisms, as well
as viruses and organella, the frequency (per 1000) of codon use in 461
organisms for which >20 genes are available was calculated by summing up
numbers of codon used. World Wide Web clients, such as NCSA Mosaic and
Netscape, may be used to query this file. A user can display a codon usage
table by clicking an anchor for selecting species or searching with species'
name (Fig.
1
).
Complete form of the database is available by anonymous ftp from DDBJ:
ftp://ftp.nig.ac.jp/pub/db/codon/GB90.
The file README contains the latest information on the database in plain text
format.
The frequencies of codon use in 461 organisms for which >20 genes are available
can be accessed on the following WWW server:
http://tisun4a.lab.nig.ac.jp/codon/CUTG.html.
Comments on the database can be sent to cutg{at}lab.nig.ac.jp by e-mail.
The authors wish to thank Dr Y. Ugawa at the DNA Information and Stock Center,
National Institute of Agrobiological Resources, for help in constructing the
database. This work was supported by a grant-in-aid for creative basic research (Human Genome Project) and for
scientific research on a priority area (Genome Informatics) and by a grant-in-aid of scientific research from the Ministry of Education, Science
and Culture of Japan.
REFERENCES
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